Chemical Physics Letters (v.502, #1-3)

Contents (iii-ix).

Display Omitted► Reviewing recent applications and validations of the Minnesota density functionals (especially the M06 family). ► Emphasizing successes in nanochemistry, organic, inorganic, and biological chemistry, and catalysis. ► Highlighting the broad accuracy of the Minnesota functionals.We discuss and review selected recent applications and validations of the Minnesota density functionals, especially the M06 family, emphasizing nanochemistry, organic, inorganic, and biological chemistry, and catalysis and highlighting the broad accuracy of these functionals as compared to previous popular functionals for thermochemistry, kinetics, and noncovalent interactions.

Renormalization of the rotational constants of an ammonia molecule seeded into a 4He droplet by Antonio Gamboa Suárez; Jordan A. Ramilowski; R.M. Benito; David Farrelly (14-22).
Projection of the wave function for the | 1 0 0 1 〉 state of the 4He–NH3 dimer. The wave function was obtained using the adiabatic diagonalization procedure described in the text with R 0 = 9.1 a . u . The adiabatic node is seen to oscillate around the node appropriate to the isotropic complex.Display Omitted► Calculations find quantitative agreement with experiments for the renormalization of the rotational constant of an ammonia molecule in a helium 4 droplet. ► Supports the conclusions of the recent experimental study that a previous experiment over-estimated the extent of renormalization. ► Extends adiabatic node diffusion Monte Carlo method beyond linear molecules.The solvation dynamics of an ammonia molecule seeded into a droplet of 4He containing N = 1 – 25 4He atoms are studied using the diffusion Monte Carlo method. Excited states are computed using the fixed-node procedure. The reduction of ∼3–5% in the rotational constants of the molecule is in quantitative agreement with recent experiments of Slipchenko and Vilesov (2005) and disagrees with the much larger ∼25% reduction originally reported by Behrens et al. (1998) .

Display Omitted► First detail theoretical study using ab initio and DFT theory. ► Potential energy surface of the reaction shows an indirect mechanism with the involvement of pre- and post-reaction complexes. ► Total rate constant and rate constants for each channel are reported in a wide temperature range of 250–1000 K. ► Calculated rate constant values are in good agreement with the available experimental results. ► Thermochemistry of the reaction is also reported.Kinetics and thermochemistry of the gas-phase reactions between (CF3)2CHOCH3 and OH radical are studied using the G2(MP2) and hybrid density functional model MPWB1 K method. The hydrogen abstraction reaction from the –CH3 group is found to be the dominant reaction channel, whereas hydrogen abstraction from the –CH site become equally important at higher temperature range. The G2(MP2) calculated total rate constant value of 1.88 × 10−13  cm3  molecule−1  s−1 at 298 K is found to be in very good agreement with the experimental value of (2.25 ± 0.04) × 10−13  cm3  molecule−1  s−1. The rate constant value obtained from the MPWB1K method (5.53 × 10−13  cm3  molecule−1  s−1) is found to be somewhat higher than the available experimental result.

Characterization by mass spectrometry and IRMPD spectroscopy of the sulfoxide group in oxidized methionine and related compounds by Marta Ignasiak; Debora Scuderi; Pedro de Oliveira; Tomasz Pedzinski; Yamina Rayah; Chantal Houée Levin (29-36).
Display Omitted► The IR S=O bond signature is established by IRMPD and DFT calculations around 1000 cm−1. ► Not only the 2-electron oxidation, but also one-electron oxidation by OH radicals of a peptide containing methionine leads to the sulfoxide form. ► 2 the one electron oxidation of the dipeptide Met Lys was studied by mass spectrometry.Methionine protein residues are prone to oxidation. To unravel the controversy about the mechanism of its one-electron oxidation, we characterised the main biological product, methionine sulfoxide, using mass spectrometry and IR multiple photon dissociation spectroscopy.Gas phase IR spectra in the 800–2000 cm−1 range of protonated methionine and its sulfoxide were recorded and compared to those computed for the lowest energy structures. The signature of the S=O bond was clearly identified at around 1000 cm−1. Oxidation of methionine–lysine dipeptide by OH radicals in the presence of catalase revealed the formation of methionine sulfoxide upon one-electron oxidation.

Hyperfine structure of the a 1 Δ g - X 3 ∑ g - transitions of 16O17O, 17O18O and 17O2 by CRDS at 80 K by Samir Kassi; Olga Leshchishina; Iouli E. Gordon; Shanshan Yu; Alain Campargue (37-41).
Display Omitted► The CRDS spectrum of the a 1 Δ g - X 3 ∑ g - band of 16O17O, 17O18O and 17O2 has been recorded at 80 K. ► The nuclear hyperfine structure of the transitions could be partly resolved. ► The hyperfine parameter coupling in the a 1 Δ g state has been derived.The high sensitivity absorption spectrum of the a 1 Δ g - X 3 ∑ g - band of 16O17O, 17O18O and 17O2 has been recorded by CW-Cavity Ring Down Spectroscopy near 1.27 μm. The spectra were obtained between 7640 and 7917 cm−1 with a 17O-enriched sample at room temperature and at 80 K. Due to the I  = 5/2 nuclear spin of the 17O atom, the nuclear hyperfine structure of the transitions could be partly resolved at low temperature. The parameter coupling of the nuclear spin to the electronic angular momentum in the a 1Δg state has been derived for the three studied isotopologues of oxygen.

The rotational spectrum of trans-DCOOD: Lamb-dip measurements, THz spectroscopy and quantum-chemical calculations by Gabriele Cazzoli; Cristina Puzzarini; Stella Stopkowicz; Jürgen Gauss (42-47).
Display Omitted► Rotational spectrum of trans-DCOOD recorded at sub-Doppler resolution: the Lamb-dip technique. ► The hyperfine structure due to the deuterium nuclei resolved and accurate hyperfine constants derived. ► High-level quantum-chemical calculations at the coupled-cluster level using large atomic-orbital basis sets of the hyperfine parameters: essential support to experiment. ► Doppler-limited measurements in the THz frequency domain.The rotational spectrum of the bi-deuterated isotopologue of trans-formic acid, trans-DCOOD, was recorded at sub-Doppler resolution in the millimeter- and sub-millimeter-wave region using the Lamb-dip technique. The hyperfine structure due to the deuterium nuclei could be resolved and accurate hyperfine constants were derived. The experimental determination of the deuterium quadrupole-coupling constants was supported by high-level quantum-chemical calculations at the coupled-cluster level using large atomic-orbital basis sets. The Lamb-dip measurements were also supplemented by THz Doppler-limited measurements in order to extend the predictive capability of the available spectroscopic parameters to higher frequencies, i.e., up to 5 THz.

Display Omitted► Quasi-classical trajectory dynamics of the light-heavy- heavy H + CCl4 reaction. ► Polanyi rules in polyatomic reactions. ► In the H + CCl4 reaction, translational energy is more effective than an equivalent amount of vibrational energy. ► Role of the intramolecular vibrational redistribution (IVR) in the reaction.The effects of vibrational versus translational energies in the dynamics of the light–heavy–heavy H + CCl4 reaction were examined by performing trajectory calculations on an analytical surface developed by our group. For this ‘early transition state’ reaction, translational energy was found to be considerably more effective at driving the reaction than an equivalent amount of vibrational energy, thus extending the validity of Polanyi rules to this polyatomic system. This behaviour was explained on the basis of there being little or negligible intramolecular vibrational redistribution in the CCl4 reactant before collision with the H atom.

On the stability of isolated Pt ( SCN ) 4 2 - dianions in vacuo and action spectroscopy experiments by Christian Nygaard Hansen; Maj-Britt Suhr Kirketerp; Mads Bejder Kristensen; Steen Brøndsted Nielsen; Kristian Støchkel; Jean Ann Wyer (53-56).
Display Omitted► Isolated Pt ( SCN ) 4 2 - dianions in vacuo are long-lived on the seconds time scale. ► UV excitation of Pt ( SCN ) 4 2 - leads dominantly to electron loss. ► The absorption by Pt ( SCN ) 4 2 - is unperturbed by a solvent.Tetrathiocyanoplatinate(II), Pt ( SCN ) 4 2 - , isolated in vacuo was subjected to a range of experiments. From storage ring measurements the dianions were found to be stable on the seconds time scale. At another instrumental setup, ions were photoexcited with UV light, and the dominant decay channel was electron detachment. The yield of Pt ( SCN ) 4 - monoanions as a function of wavelength provided the action spectrum. Maximum absorption occurs at ∼240 nm, and the spectrum is similar to the absorption spectrum of Pt ( SCN ) 4 2 - in methanol solution, which implies that a solvent perturbs the ground state and the electronically excited state in the same manner.

Temperature dependence of vibrational relaxation of the OH bending excitation in liquid H2O by Satoshi Ashihara; Sachi Fujioka; Kazunori Shibuya (57-62).
Display Omitted► The energy relaxation of the OH bending vibration in pure liquid H2O was found to show anomalous temperature dependence. ► The population lifetime increases from 170 fs at T  = 295 K to 250 fs at T  = 348 K. ► The observed temperature dependence supports the relaxation scenario that the bend vibrational energy is dominantly transferred to librational motions.Mid-infrared pump–probe spectroscopy measurements of the OH bending vibration in pure liquid water were performed at different temperatures. The population lifetime increases from 170 ± 15 fs at T  = 295 K to 250 ± 15 fs at T  = 348 K. This temperature dependence can be explained by the decrease in the spectral overlap between the OH bending and the high-frequency librational modes, supporting the relaxation scenario that the bend vibrational energy is dominantly transferred to librational motions. It was also found that the temperature dependence becomes absent below room temperature, the possible origin for which is discussed.

Periodic density functional study of Co3O4 surfaces by Alejandro Montoya; Brian S. Haynes (63-68).
Display Omitted► Spin polarised density functional theory within the GGA + U approach has been used to study surface slabs of cobalt oxide Co3O4. ► At any given condition of temperature and oxygen partial pressure, the various (1 1 0) and (1 1 1) terminations of Co3O4 are always less stable than the most stable (1 0 0) terminations. ► Cobalt atoms at the surface of the Co3O4(1 0 0) slabs exhibit a redistribution of the density of states compared with those in the bulk, increasing the population at the Fermi level and changing the insulator characteristic of the bulk to give a semimetallic characteristic to the (1 0 0) slabs.Density functional theory within the GGA + U framework has been used to study surface slabs of Co3O4. The thermodynamic stability of the surfaces was assessed in terms of the surface free energy as a function of oxygen potential. At any given condition of temperature and oxygen partial pressure, the various (1 1 0) and (1 1 1) terminations are always less stable than the most stable (1 0 0) terminations. Under oxygen-rich conditions, a Co3O4 (1 0 0) surface exposing Co in octahedral positions is thermodynamically preferred, while under oxygen-lean conditions, a Co3O4 (1 0 0) surface exposing Co atoms in tetrahedral and octahedral positions is preferred.

Display Omitted► Photoacoustic assessment of nonradiative relaxation and diffusion times. ► Rare earth ions act as glass network modifiers decreasing bonds connectivity. ► Heat exchange times depends on the shape and size of particles.Nonradiative relaxation time (τ) and characteristic diffusion time ( τ β ) of Nd, Er and Co doped low silica calcium aluminosilicate (LSCA) glasses were assessed by means of photoacoustic spectroscopy. The results are interpreted in terms of frequency dependence predicted by the theory of Rosencwaig and Gersho. Whereas τ varied between 7.2 ms and 36 ms, the values of τ β lied between 0.25 ms and 0.7 ms. For the neodymium doped LSCA glass, a decrease in τ β was observed as the ion concentration was increased. The results indicates that rare earth ion acts as network modifier, disrupting the glass lattice.

Display Omitted► Fluctuations of H2O molecules in HfF4·3H2O at different temperatures. ► Measured relaxation parameters by TDPAC. ► Measured H2O activation energy from relaxation constants. ► Direct evidence of one loosely bound H2O in HfF4·3H2O.Fluctuations of H2O molecules in the crystallized sample HfF4·3H2O have been studied in the temperature range 298–363 K by perturbed angular correlation (PAC) technique. In this crystal, apart from static components, time dependent relaxed component has been observed at these temperatures. The relaxation constants are found to increase with temperature up to 353 K following the Arrehenius equation and then decreases at 363 K where a chemical transformation in the sample has been observed. The time dependent relaxed component has been attributed to the fluctuation of H2O molecule in HfF4·3H2O. From the measured relaxation constants at different temperatures, activation energy for the H2O molecule has been found to be 0.15(1) eV.

A theoretical spectroscopy investigation of bifunctional platinum-bridged diarylethenes by Aurélie Perrier; François Maurel; Ilaria Ciofini; Denis Jacquemin (77-81).
Display Omitted► Accurate ab intio tools are used to investigate the spectral and photophysical properties of coupled photochromes. ► Very good agreement with experiment is reached for IR, NMR and UV/Vis spectra. ► The second electro-cyclisation does not proceed through the usual singlet path. ► The platinum-containing bridge allows an efficient communication between the two switches.This Letter is a theoretical investigation of the ground and excited-state properties of diarylethenes coupled through a platinum-containing bridge. Our simulations are performed using (Time-Dependent) Density Functional Theory in conjunction with the Polarisable Continuum Model and aim at characterising the coupling between the two photochromes. It turns out that theory provides results in very good agreement with experiment for the IR, NMR and UV/Vis spectroscopies. The states and orbitals involved in the relevant UV transitions are analysed, allowing to obtain insights regarding the successive electro-cyclisations, the second probably using a triplet pathway.

Display Omitted► Single-, poly-crystalline and glassy nanoparticles appears depending on cooling rate. ► The solidification point decreases with increasing cooling rate. ► CCT diagram shows correlation between cooling rate and nanoparticle structure plainly.The effect of the cooling rate on the solidification behavior of metal nanoparticles is investigated by molecular dynamics simulation. The structure of molybdenum nanoparticles varies with the cooling rate. That is, single-crystalline, polycrystalline then glassy nanoparticles are obtained as the cooling rate is increased from 2.0 × 1010 to 1.0 × 1013  K/s. The solidification point decreases with increasing cooling rate then drops rapidly at a cooling rate on the order of 1012  K/s. These results are summarized in a continuous cooling transformation (CCT) diagram, in which regions corresponding the liquid, single-crystalline, polycrystalline and glassy structures appear.

A pulsed neutron diffraction study of the topological defects presence in carbon nanohorns by Lukasz Hawelek; Wojciech Wrzalik; Aleksander Brodka; John C. Dore; Alex C. Hannon; Sumio Iijima; Masako Yudasaka; Tomonori Ohba; Katsumi Kaneko; Andrzej Burian (87-91).
Display Omitted► Pulsed neutrons diffraction provided information about the structure of nanohorns. ► Molecular dynamics modelling allowed revealing topological defects in nanohorns. ► Pulsed neutrons diffraction yielded the pair correlation function of good resolution. ► This procedure will be useful for carbon nanomaterials produced on a mass scale.The structure of single-wall carbon nanohorns has been studied using pulsed neutron diffraction and molecular dynamics. The collected diffraction data have been converted to a real-space representation in the form of the pair correlation function. For computer-generated models consisting of nanocones and single-wall carbon nanotubes of the perfect hexagonal structure and 20–30 Å in diameter, the computed diffracted intensities and pair correlation functions are in reasonable agreement with the experimental data. For larger nanohorns of 50 Å diameter, Stone–Wales, mono-vacancy and di-vacancy defects have been introduced to fit the experimental data.

Display Omitted► ATR-FTIR of perchlorate coordinated on Mn(III)TPP. ► ATR-FTIR of perchlorate anionic solutions. ► The effects of aqueous environment on the perchlorate IR lineshape. ► Hydration dynamics around the perchlorate revealed by using the model frequency-frequency correlation function.The effects of aqueous environments on the perchlorate infrared lineshape were investigated in various ionic solutions, including a polymeric polyvinyl chloride membrane and perchlorate coordinated to manganese(III) porphyrin, using the model frequency–frequency correlation function (FFCF). The perchlorate ligand moiety is considered a useful infrared probe in aqueous nanoscopic environments. We observed an asymmetric mode of the ligated perchlorate, in which the lineshape had a smaller bandwidth and faster dynamics than that of a 1 M perchlorate aqueous solution. In the 6 M solutions, we observed at least two conformations with faster dynamics than that of the 1 M solution, regardless of whether it was in the heterogeneous polymer matrix.

Display Omitted► Electronic property of CNTs-confined nanocatalysts. ► Catalytic effect of CNTs-confined nanocatalysts in heterogeneous catalytic reaction systems. ► Conversion from ozone decomposition to hydroxyl radical generation over catalyst nanoparticle in the channel of CNTs.We investigated the catalytic effect of CuO nanoparticles confined in carbon nanotubes using molecular dynamics simulations and density functional theory calculations. Ozone decomposition and hydroxyl radical generation were used as the probe reactions to investigate the catalytic behavior of catalyst. The effects of the confined environment of carbon nanotubes induced more reactants into the channel. Interface interactions between reactants and CuO nanoparticles in the channel and charge transfer accelerated the decomposition of ozone into oxygen molecule and atomic oxygen species. The atomic oxygen species then interacted to water molecule to generate hydroxyl radicals, which were truly identified by electron paramagnetic resonance (EPR) technique.

Effective and efficient purification of single-wall carbon nanotubes based on hydrogen treatment by Leimei Sheng; Lei Shi; Kang An; Liming Yu; Yoshinori Ando; Xinluo Zhao (101-106).
Display Omitted► We provide an effective and efficient method to get high-purity SWCNTs prepared by hydrogen arc discharge. ► Small SWCNTs can survive during the purification processes, and the purified SWCNTs possess high-crystallinity and escape obvious damage. ► A novel method used to prepare nanocatalyst (such as Pt, Pd and/or Rh) has been proposed.A simple, effective and efficient purification method for single-wall carbon nanotubes (SWCNTs) prepared by hydrogen arc discharge has been developed. Hydrogen treatment has been used to remove the amorphous carbon and graphene sheets encapsulating Fe catalyst nanoparticles. The exposed Fe nanoparticles can be easily dissolved in concentrated hydrochloric acid. Carbon content higher than 99 wt.% can be achieved. The small SWCNTs with a diameter of 0.9 nm are found to survive during the purification processes. This new purification method enables us to obtain purified SWCNTs with high-crystallinity and without obvious damage.

Display Omitted► DNA breathing dynamics. ► Rouse model. ► Fluorescence correlation spectroscopy. ► Random process.We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is modeled as a one dimensional Rouse chain confined at both the ends. The bubble is formed when the transverse displacement of the chain attains a critical value. This simple model effectively reproduces the autocorrelation function for the tagged base pair in the DNA strand as measured in the seminal single molecule experiment by Altan-Bonnet et al. (2003) . Our model goes beyond a single reaction coordinate description by incorporating the chain dynamics through a confined Rouse chain and thus considers the collective nature of the dynamics. Our model also shows that the autocorrelation function is very sensitive to the relaxation times of the normal modes of the chain, which is obvious since the fluctuation dynamics of the bubble has the contribution from the different normal modes of the chain.

Display Omitted► Significant charge delocalization for bound Cl ions in ClC Cl transport proteins. ► Important sinks of charges: Cl solvation shells and the gating residue E148. ► Extensive anion-pi charge transfer found along the translocation path. ► An additional binding site for Cl suggested by DFT geometry optimizations.Density functional theory calculations were carried out employing a set of truncated model systems for the EcClC Cl transport protein and mutants. Geometry optimizations implied a possible additional binding site near the residue R147. Analysis based on the Löwdin and Natural charge models showed that significant (about 30%) charges on the bound Cl ions were smeared out among the solvation shells and the gating residue E148, whose delocalized pi bonds provide good accommodations for the transferred charges. The extensive anion-pi charge transfer along the Cl translocation path might help to smooth/level the energy profiles for Cl transport.

Hole mobility measurement of 4,4′-Bis[N-(1-naphthyl)-N-phenylamino]-biphenyl by dark injection method by Takayuki Chiba; Ken-ichi Nakayama; Yong-Jin Pu; Tatsuo Nishina; Masaaki Yokoyama; Junji Kido (118-120).
The hole carrier mobility of deposited thin film composed of 4,4′-Bis[N-(1-naphthyl)-N-phenylamino]-biphenyl (NPD) was measured using the dark injection (DI) method. The mobility basically agreed with that measured by the time-of-flight method. We also evaluated the effect of a hole injection barrier on the estimated mobility, using several surface treatments of indium–tin oxide anode.Display Omitted► The hole mobility of organic thin film was measured using the dark injection method. ► An improved bridge circuit achieved faster response time. ► The mobility agreed with that measured by the time-of-flight method.The hole carrier mobility of deposited thin film composed of 4,4′-Bis[N-(1-naphthyl)-N-phenylamino]-biphenyl (NPD) was measured using the dark injection method. An improved bridge circuit achieved faster response time, which enabled the evaluation of practical hole transporting material with high hole mobility, using thin vacuum deposited film. The mobility basically agreed with that measured by the time-of-flight method. We also evaluated the effect of a hole injection barrier on the estimated mobility, using several surface treatments of indium–tin oxide anode. The results indicated that increasing barrier height decreases the estimated mobility; however, its effect was relatively small.

Display Omitted► A novel method for exciting 14N overtone transitions. ► Polarization transfer from proton ensures high sensitivity. ► Possibility of converting the pulse sequence as a 2D experiment built in. ► 14N–1H dipolar coupling and 14N–1H shift correlation information can be obtained from the same pulse sequence. ► Extends the use of 14N NMR spectroscopy.For studying systems containing nitrogen, limited use of 14N NMR spectroscopy has been made because of the large quadrupolar interaction experienced by the 14N nucleus and the absence of a central transition. To overcome the above problem, use of overtone spectroscopy has been suggested. Though this approach has limited applicability for powder samples due to second order quadrupole broadening, it is useful for studying oriented samples and single crystals. Here, we demonstrate the use of the recently proposed dipolar assisted polarization transfer (DAPT) pulse scheme for exciting the overtone transitions. The pulse sequence may also be utilized as a two-dimensional experiment to obtain 1H–14N dipolar couplings and 1H chemical shifts.

Display Omitted► The free electron on a quasi-infinite helix demonstrates the basic selection rules governing the magneto-optical properties of a chiral molecular system. ► Here we explore from this point of view the non-linear optical inverse Faraday effect and the inverse magnetochiral effect. ► It is shown that in these cases definite selection rules also depend on the long-wavelength approximation.The interplay of chirality and magnetism is of fundamental physical interest. A free electron on a helix with periodic boundary conditions is possibly the simplest model exhibiting both chirality and orbital paramagnetism. In a previous report we have studied with this model the relation between natural circular, magnetic circular and magnetochiral dichroism. Here we extend our investigation to the second-order nonlinear optical phenomena designated as the inverse Faraday effect and as the inverse magnetochiral effect. Both effects manifest themselves as a radiation-induced time-independent magnetic field which lifts the magnetic degeneracy of the system. While the inverse Faraday effect is circular differential, the comparatively much weaker inverse magnetochiral effect is independent of the polarization of the incident radiation.

Display Omitted► Enhanced sampling Monte Carlo simulation by dynamic non-Boltzmann weight factor. ► Energy Landscape Paving, Basin Paving, Basin Hopping. ► Folding and unfolding of RNA hairpin.Conformational landscape of RNA T-loop hairpin has been investigated by Energy Landscape Paving (ELP) and Basin Paving (BP) Monte Carlo simulations. Both ELP and BP simulations use memory of the simulation to increase the probability of the states less visited. The unfolded structures of the RNA were obtained from the folded one by ELP method. Structures were folded from extended structures by BP method. Choice of different parameters, including the use of the end-to-end distance of RNA as a memory term, in the simulations to accelerate sampling is discussed. It has been found that both ELP and BP are highly efficient techniques for unfolding and folding RNA T-loop hairpin.

Display Omitted► Coupling dependent intensity correction factor. ► Accurate measurement of homo and heteronuclear couplings. ► Simplification of the complex multiplet pattern. ► Phase sensitive double quantum refocusing. ► Higher quantum refocusing with heteronuclear decoupling.The ω1-heterodecoupled-13C-filtered proton detected NMR experiments are reported for the accurate quantification of enantiomeric excess in chiral molecules embedded in chiral liquid crystal. The differential values of both 1H–1H and 13C–1H dipolar couplings in the direct dimension and only 1H–1H dipolar couplings in the indirect dimension enable unraveling of overlapped enantiomeric peaks. The creation of unequal 13C-bound proton signal for each enantiomer in the INEPT block and non-uniform excitation of coherences in homonuclear multiple quantum experiments do not yield accurate quantification of enantiomeric excess. In circumventing these difficulties, a coupling dependent intensity correction factor has been invoked.